2026-09-23 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY audit_author citation citation_author em_admin em_author_list _audit_author.name _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update _em_author_list.author EXPERIMENTAL_SUMMARY citation citation_author em_admin em_author_list _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update _em_author_list.author DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update RCSB RCSB 2025-01-13 2025-02-19 2025-02-19 2026-09-23 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM131860 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM047477 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM098399 United States Structure of native Drosophila melanogaster DLST Venette-Smith NL Vishwakarma RK Dollinger R Schultz J Venkatakrishnan V Babitzke P Anand G Gilmour DS Armache J-P Murakami KS chromatin, succinyltransferase, DLST, GENE REGULATION Venette-Smith NL Vishwakarma RK Venkatakrishnan V Dollinger R Schultz J Babitzke P Anand G Gilmour DS Armache JP Murakami KS Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster. Nat Commun UK 17 2026 42711332 doi:10.1038/s41467-026-75963-0 2041-1723 9mu6 FULLOVERLAP EMDB EMD-48621 associated EM volume
Structure of native Drosophila melanogaster DLST
 Natively purified DLST from Drosophila melanogaster Natively purified DLST from Drosophila melanogaster 0 1
This entry represents a native dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial, purified from Drosophila melanogaster embryos
Drosophila melanogaster 650 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial Drosophila melanogaster 0.025756025000000002 24 LEVO GTRSEQRVKMNRMRLKIAARLKDAQNTCAMLTTFNEVDMSYAMDFRKQNLDAFTKKYGIKFGFMSIFAKASAYALQDQPV VNAVIDGTDIVYRDYVDISVAVATPRGLVVPVIRNVEGMNYADIEIALAGLADKARRDAITVEDMDGGTFTISNGGVFGS LMGTPIINPPQSAILGMHGIFERPIAVKGEVKIRPMMYIALTYDHRIIDGREAVLFLRKIKAAVENPAIIVAGL Q9VGQ1 2.3.1.61 singleParticle particle 1.0 7.5 150.0 NaCl Sodium chloride 10.0 HEPES-HCl HEPES 5.0 Glycerol Glycerol 1.0 EDTA EDTA 350.0 FLAG FLAG peptide
10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor
 Quantifoil GOLD 200 GOLD HOLEY GLOW DISCHARGE ETHANE 100 4 FEI VITROBOT MARK IV
double FLAG-tagged Pol II subunit Rpb1 was used for purification of Pol II complexes. We aimed to purify Pol II in tandem with nucleosomes. DLST was co-purified with this sample
 TFS TALOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1.0 2.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 4096 4096 4 31103 50.65
Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was achieved by extracting particles in box size 440x440 and Fourier-cropping it to box size 360x360
 1 70106
Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (70,106) is the starting number of particles after initial cleanup and 3D classification of the data.
 cryoSPARC 4.3.1
'Patch CTF Estimation' in cryoSPARC
PHASE FLIPPING AND AMPLITUDE CORRECTION 'Ab initio' function in cryoSPARC 1 O BACK PROJECTION 3.66 FSC 0.143 CUT-OFF cryoSPARC 4.3.1 23543 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1
'Non-Uniform Refinement' in cryoSPARC
 emd_48621.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z 0.0 1.2063622 0.0041118623 0.033465113 1.1538 1.1538 1.1538 0.3 AUTHOR Refined, unsharpened Coulomb potential density map. Particles extracted in 440x440 Fourier cropped to 360x360. Q9VGQ1 AlphaFold in silico model AB INITIO MODEL
The model was built without a template. AlphaFold2 models for individual subunits were inserted into the density, and further optimized in the density using rigid-body fit. Then, in Coot, the models were Real-space refined. For the final model optimization, phenix.real_space_refine was used
50.0 emd_48621_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -1.0887507 3.1167371 0.0041118623 0.056096118 1.1538 1.1538 1.1538 AUTHOR Refined, sharpened Coulomb potential density map. B-factor = -102.6. Particles extracted in 440x440 Fourier cropped to 360x360. emd_48621_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -0.3539386 1.2686318 0.0011801032 0.046911687 1.1538 1.1538 1.1538 AUTHOR Half map 2 emd_48621_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 415.368 415.368 415.368 90.0 90.0 90.0 X Y Z -0.3277642 1.4110234 0.0011740413 0.04694255 1.1538 1.1538 1.1538 AUTHOR Half map 1